Our work demonstrates how combining bulked segregation-based RNA-seq with high-throughput SNP arrays enables fast, cost-effective, and yet reliable identification of the most informative (population-specific) markers among hundreds of thousands of in-silico SNPs.
The method used for genotyping is well established in molecular epidemiological studies and the msp2 gene has proven to be the most informative marker of parasite population diversity [29].
The correlation between true and imputed genotypes (rTG,IG) based on the 50 most informative animals as reference population is compared with rTG,IG obtained with 50 randomly selected reference animals.
The full SLI has 29 items, but only a subset of items believed to be most informative for this study population was used to derive the early and current SEP.
The full Standard of Living Index has a large number of items (29 in total), but we used the 14 items (quality of house; toilet facilities; sources of lighting and drinking water; land ownership; and possession of a clock, radio, television, bicycle, motorcycle, car, tractor, refrigerator, or telephone) that we believed to be most informative for our study population.
We also used Lh/Lmax, the ratio of Lh to the greatest likelihood among all sampled populations [ 38], which has greater power and is most informative when all source populations have been sampled.
The most informative linear model described only a population difference: the Laguna Mountain population displayed more restlessness than the population from UC-San Diego (with Laguna Mountain as reference: effect of population = -1299.4, p = 0.054; R = 0.102).
We were able to build a superior predictor by prioritizing the most informative strains in a viral population and crafting a more complex information merging procedure based on a set kernel, rather than uniformly processing all strains occurring in the population and merging information by using simple cutoffs.
We have shown that the greatest relative risk occurs when risk alleles are present on chromosomes 1 and 9. Finally based on an analysis of the processes in which candidate genes are involved, we suggest that processes rather than genes are the most informative way to compare different populations, and have shown that such comparisons reduce discordance by approximately 19%.
When several studies were based on the same patient population, only the most informative study was included.
To discriminate among these possibilities, further studies are needed, and along these lines we expect that mRNA profiling of specific cell populations will be most informative (e.g., using flow cytometry or laser capture microdissection) [ 13].
